Avoid breaking cross-compiled ACPI tools builds by rearranging the
handling of kernel header files.

This patch also contains OUTPUT/srctree cleanups in order to make above fix
working for various build environments.

Fixes: e323c02d (ACPICA: MSVC9: Fix <sys/stat.h> inclusion order issue)
Reported-and-tested-by: Yisheng Xie <xieyisheng1@huawei.com>
Reported-by: Andy Shevchenko <andy.shevchenko@gmail.com>
Signed-off-by: Lv Zheng <lv.zheng@intel.com>
[ rjw: Changelog ]
Signed-off-by: Rafael J. Wysocki <rafael.j.wysocki@intel.com>